@article{DBLP:journals/ijfcs/BrijderEMR11,
  author    = {Robert Brijder and
               Andrzej Ehrenfeucht and
               Michael G. Main and
               Grzegorz Rozenberg},
  title     = {A Tour of reaction Systems},
  journal   = {International Journal of Foundations of Computer Science},
  volume    = {22},
  number    = {7},
  year      = {2011},
  pages     = {1499-1517},
  ee        = {http://dx.doi.org/10.1142/S0129054111008842},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{DBLP:journals/tcs/EhrenfeuchtR07,
  author    = {Andrzej Ehrenfeucht and
               Grzegorz Rozenberg},
  title     = {Events and modules in reaction systems},
  journal   = {Theoretical Computer Science},
  volume    = {376},
  number    = {1-2},
  year      = {2007},
  pages     = {3-16},
  ee        = {http://dx.doi.org/10.1016/j.tcs.2007.01.008},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{DBLP:journals/entcs/ThanhKP02,
  author    = {C{\'e}cile Bui Thanh and
               Hanna Klaudel and
               Franck Pommereau},
  title     = {Petri nets with causal time for system verification},
  journal   = {Electronic Notes in Theoretical Computer Science},
  volume    = {68},
  number    = {5},
  year      = {2002},
  pages     = {85-100},
  ee        = {http://dx.doi.org/10.1016/S1571-0661(04)80521-8},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{AbdullaCJT00,
  author    = {Parosh Aziz Abdulla and
               Karlis Cerans and
               Bengt Jonsson and
               Yih-Kuen Tsay},
  title     = {Algorithmic Analysis of Programs with Well Quasi-ordered
               Domains},
  journal   = {Information and Computation},
  volume    = {160},
  number    = {1-2},
  year      = {2000},
  pages     = {109-127},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{FinkelS01,
  author    = {Alain Finkel and
               Philippe Schnoebelen},
  title     = {Well-structured transition systems everywhere!},
  journal   = {Theoretical Computer Science},
  volume    = {256},
  number    = {1-2},
  year      = {2001},
  pages     = {63-92},
  ee        = {http://dx.doi.org/10.1016/S0304-3975(00)00102-X},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@Article{synthetic,
 author = {Serrano, Luis},
 title = {Synthetic biology: promises and challenges},
 journal = {Molecular Systems Biology},
 year = {2007},
 volume = {3},
 number = {158}
}

@article{toxicology,
author = {Schmidt, Markus and Pei, Lei},
 title = {Synthetic toxicology: where engineering meets biology and toxicology},
 journal = {Toxicological sciences : an official journal of the Society of Toxicology},
 year = {2011},
 volume = {Suppl. 1},
 number = {120},
 pages ={S204-24}
}

@article{computational,
    abstract = {{ Computational systems biology is an emerging field in biological simulation that attempts to model or simulate intra- and intercellular events using data gathered from genomic, proteomic or metabolomic experiments. The need to model complex temporal and spatiotemporal processes at many different scales has led to the emergence of numerous techniques, including systems of differential equations, Petri nets, cellular automata simulators, agent-based models and pi calculus. This review provides a brief summary and an assessment of most of these approaches. It also provides examples of how these methods are being used to facilitate drug discovery and development. }},
    address = {National Research Council, National Institute for Nanotechnology (NINT) Edmonton, Alberta, Canada T6G 2E8.},
    author = {Materi, Wayne and Wishart, David S.},
    doi = {10.1016/j.drudis.2007.02.013},
    issn = {13596446},
    journal = {Drug Discovery Today},
    keywords = {rev},
    number = {7-8},
    pages = {295--303},
    pmid = {17395089},
    posted-at = {2011-11-12 01:25:57},
    priority = {2},
    title = {{Computational systems biology in drug discovery and development: methods and applications}},
    url = {http://dx.doi.org/10.1016/j.drudis.2007.02.013},
    volume = {12},
    year = {2007}
}

@inproceedings{Basso-Blandin2012,
  author    = {Adrien Basso-Blandin and
               Franck Delaplace},
  title     = {GUBS, a behavior-based language for open system dedicated
               to synthetic biology},
  booktitle = {MeCBIC},
  year      = {2012},
  pages     = {29-47},
  ee        = {http://dx.doi.org/10.4204/EPTCS.100.3},
  crossref  = {DBLP:journals/corr/abs-1211-3476},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:journals/corr/abs-1211-3476,
  editor    = {Gabriel Ciobanu},
  title     = {Proceedings 6th Workshop on Membrane Computing and Biologically
               Inspired Process Calculi},
  booktitle = {MeCBIC},
  series    = {EPTCS},
  volume    = {100},
  year      = {2012},
  ee        = {http://dx.doi.org/10.4204/EPTCS.100},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@article{Czar2009,
abstract = {Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD (www.genocad.org) is a free web-based application to design protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the 
libraries, or reusing designs to quickly generate sets of related constructs.},
author = {Czar, Michael J. and Cai, Yizhi and Peccoud, Jean},
doi = {10.1093/nar/gkp361},
file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Czar, Cai, Peccoud - 2009 - Writing DNA with GenoCAD.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Base Sequence,DNA,DNA: chemical synthesis,DNA: chemistry,Genes, Synthetic,Genetic Engineering,Software,User-Computer Interface},
number = {Web Server issue},
pages = {W40--7},
pmid = {19429897},
title = {{Writing DNA with GenoCAD.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703884\&tool=pmcentrez\&rendertype=abstract},
volume = {37},
year = {2009}
}
@article{Bilitchenko2011,
abstract = {Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.},
author = {Bilitchenko, Lesia and Liu, Adam and Cheung, Sherine and Weeding, Emma and Xia, Bing and Leguia, Mariana and Anderson, J. Christopher and Densmore, Douglas},
doi = {10.1371/journal.pone.0018882},
file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Bilitchenko et al. - 2011 - Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
number = {4},
pages = {e18882},
pmid = {21559524},
title = {{Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084710\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2011}
}
@article{Beal2011,
author = {Beal, Jacob and Lu, Ting and Weiss, Ron},
doi = {10.1371/journal.pone.0022490},
editor = {Ben-Jacob, Eshel},
file = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Beal, Lu, Weiss - 2011 - Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks.pdf:pdf},
issn = {1932-6203},
journal = {PLoS ONE},
number = {8},
pages = {e22490},
title = {{Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks}},
url = {http://dx.plos.org/10.1371/journal.pone.0022490},
volume = {6},
year = {2011}
}
@article{Purnick2009,
abstract = {Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering. Efforts in synthetic biology have largely focused on the creation and perfection of genetic devices and small modules that are constructed from these devices. But to view cells as true 'programmable' entities, it is now essential to develop effective strategies for assembling devices and modules into intricate, customizable larger scale systems. The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies.},
author = {Purnick, Priscilla E M and Weiss, Ron},
doi = {10.1038/nrm2698},
file = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Purnick, Weiss - 2009 - The second wave of synthetic biology from modules to systems.pdf:pdf},
issn = {1471-0080},
journal = {Nature reviews. Molecular cell biology},
keywords = {bsao},
mendeley-tags = {bsao},
number = {6},
pages = {410--22},
pmid = {19461664},
shorttitle = {Nat Rev Mol Cell Biol},
title = {{The second wave of synthetic biology: from modules to systems.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19461664},
volume = {10},
year = {2009}
}

@article{pinney,
    abstract = {{The mathematical structures known as Petri Nets have recently become the focus of much research effort in both the structural and quantitative analysis of all kinds of biological networks. This review provides a very brief summary of these interesting new research directions.}},
    address = {Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K. john@bioinformatics.leeds.ac.uk},
    author = {Pinney, J. W. and Westhead, D. R. and McConkey, G. A.},
    citeulike-article-id = {273},
    citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/14641101},
    citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=14641101},
    issn = {0300-5127},
    journal = {Biochemical Society Transactions},
    keywords = {biology, net, petri, sysbio},
    number = {Pt 6},
    pages = {1513--1515},
    pmid = {14641101},
    posted-at = {2008-01-27 19:38:47},
    priority = {2},
    title = {{Petri Net representations in systems biology.}},
    url = {http://view.ncbi.nlm.nih.gov/pubmed/14641101},
    volume = {31},
    year = {2003}
}

@incollection{CardelliP09,
  added-at = {2011-09-22T00:00:00.000+0200},
  author = {Cardelli, Luca and Priami, Corrado},
  biburl = {http://www.bibsonomy.org/bibtex/20fc143882c83b3491ee5002153805ca3/dblp},
  booktitle = {The Fourth Paradigm},
  editor = {Hey, Tony and Tansley, Stewart and Tolle, Kristin M.},
  ee = {http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part2_cardelli_priami.pdf},
  interhash = {f8cdc5cb772c91659a0405a009e3fb4b},
  intrahash = {0fc143882c83b3491ee5002153805ca3},
  isbn = {978-0982544204},
  keywords = {dblp},
  pages = {99-105},
  publisher = {Microsoft Research},
  timestamp = {2011-09-22T00:00:00.000+0200},
  title = {Visualization in process algebra models of biological systems.},
  url = {http://dblp.uni-trier.de/db/books/collections/4paradigm2009.html#CardelliP09},
  year = 2009
}

@article{journals/tcsb/Cardelli05,
  added-at = {2005-12-22T00:00:00.000+0100},
  author = {Cardelli, Luca},
  biburl = {http://www.bibsonomy.org/bibtex/20e3ebf1e17c6b782a59c09d0481fc406/dblp},
  journal = {Transactions on Computational Systems Biology},
  date = {2005-12-22},
  description = {dblp},
  editor = {Priami, Corrado and Merelli, Emanuela and Gonzalez, Pedro Pablo and Omicini, Andrea},
  ee = {http://dx.doi.org/10.1007/11599128_10},
  interhash = {2848be2cdd43ed54ccd19f1789eecc1c},
  intrahash = {0e3ebf1e17c6b782a59c09d0481fc406},
  isbn = {3-540-30883-0},
  keywords = {dblp},
  pages = {145-168},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  timestamp = {2005-12-22T00:00:00.000+0100},
  title = {Abstract Machines of Systems Biology.},
  url = {http://dblp.uni-trier.de/db/journals/tcsb/tcsb3.html#Cardelli05},
  volume = 3737,
  year = 2005
}

@incollection{MadhuKrithi,
year={2003},
isbn={978-3-540-00611-4},
booktitle={Membrane Computing},
volume={2597},
series={Lecture Notes in Computer Science},
editor={PĂun, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto and Zandron, Claudio},
doi={10.1007/3-540-36490-0_24},
title={A Survey of Some Variants of P Systems},
url={http://dx.doi.org/10.1007/3-540-36490-0_24},
publisher={Springer Berlin Heidelberg},
author={Madhu, Mutyam and Krithivasan, Kamala},
pages={360-370},
language={English}
}

@article{DBLP:journals/ijfcs/PaunPRS11,
  author    = {Andrei Paun and
               Mihaela Paun and
               Alfonso Rodr\'{\i}guez-Pat{\'o}n and
               Manuela Sidoroff},
  title     = {P Systems with proteins on Membranes: a Survey.},
  journal   = {International Journal of Foundations of Computer Science},
  volume    = {22},
  number    = {1},
  year      = {2011},
  pages     = {39-53},
  ee        = {http://dx.doi.org/10.1142/S0129054111007812},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{DBLP:journals/tcs/DanosL04,
  author    = {Vincent Danos and
               Cosimo Laneve},
  title     = {Formal molecular biology},
  journal   = {Theoretical  Computer Science},
  volume    = {325},
  number    = {1},
  year      = {2004},
  pages     = {69-110},
  ee        = {http://dx.doi.org/10.1016/j.tcs.2004.03.065},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
